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- PDB-1m78: CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH DIHYDRO-N... -

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Basic information

Entry
Database: PDB / ID: 1m78
TitleCANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NADPH) AND 5-CHLORYL-2,4,6-QUINAZOLINETRIAMINE (GW1225)
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / ANTIFUNGAL TARGET / REDUCTASE
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-CHLORYL-2,4,6-QUINAZOLINETRIAMINE / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.71 Å
AuthorsWhitlow, M. / Howard, A.J. / Kuyper, L.F.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: X-Ray Crystallographic Studies of Candida Albicans Dihydrofolate Reductase. High Resolution Structures of the Holoenzyme and an Inhibited Ternary Complex.
Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Kuyper, L.F. / Baccanari, D.P. / Fling, M.E. / Tansik, R.L.
#1: Journal: J.Med.Chem. / Year: 2001
Title: X-Ray Crystal Structures of Candida Albicans Dihydrofolate Reductase: High Resolution Ternary Complexes in which the Dihydronicotinamide Moiety of Nadph is Displaced by an Inhibitor
Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Chan, J.H. / Baccanari, D.P. / Tansik, R.L. / Hong, J.S. / Kuyper, L.F.
#2: Journal: J.Med.Chem. / Year: 1995
Title: Selective Inhibitors of Candida Albicans Dihydrofolate Reductase: Activity and Selectivity of 5-(Arylthio)-2,4-Diaminoquinazolines
Authors: Chan, J.H. / Hong, J.S. / Kuyper, L.F. / Baccanari, D.P. / Joyner, S.S. / Tansik, R.L. / Boytos, C.M. / Rudolph, S.K.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Characterization of Candida Albicans Dihydrofolate Reductase
Authors: Baccanari, D.P. / Tansik, R.L. / Joyner, S.S. / Fling, M.E. / Smith, P.L. / Freisheim, J.H.
History
DepositionJul 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2996
Polymers44,3892
Non-polymers1,9104
Water6,071337
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A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1503
Polymers22,1951
Non-polymers9552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1503
Polymers22,1951
Non-polymers9552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.910, 67.280, 38.490
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDihydrofolate reductase is active as a monomer.

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / DHFR


Mass: 22194.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: DFR1 / Plasmid: P1869 / Species (production host): Escherichia coli / Cellular location (production host): cytoplasm / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22906, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CLZ / 5-CHLORYL-2,4,6-QUINAZOLINETRIAMINE


Mass: 209.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8ClN5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: liquid diffusion / pH: 7.5
Details: dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH), 5-chloryl-2,4,6-quinazolinetriamine (GW1225), PEG-3350, Potassium 4-morphilineethanesulfonic acid (MES), dithiothreitol (DTT), pH ...Details: dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH), 5-chloryl-2,4,6-quinazolinetriamine (GW1225), PEG-3350, Potassium 4-morphilineethanesulfonic acid (MES), dithiothreitol (DTT), pH 7.50, LIQUID DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Mar 29, 1988 / Details: Huber graphite MONOCHROMATOR
RadiationMonochromator: HUBER GRAPHITE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 37244 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.118 % / Biso Wilson estimate: 34.35 Å2 / Rmerge(I) obs: 0.0537 / Rsym value: 0.0537 / Net I/σ(I): 17.6
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.2337 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4052 / Rsym value: 0.2337 / % possible all: 60.55

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Processing

Software
NameClassification
X-GENdata reduction
FRODOmodel building
PROFFTrefinement
X-GENdata scaling
RefinementMethod to determine structure: DIRECT REPLACEMENT
Starting model: CANDIDA ALBICANS DHFR (PDB ENTRY 1AI9)

1ai9


Resolution: 1.71→10 Å
Isotropic thermal model: Konnert, J.H. & Hendrickson, W.A. (1980) Acta Crystallogr. A A36, 344.
σ(F): 2 / σ(I): -3
Stereochemistry target values: Hendrickson, W.A. (1985) Methods Enzymol. 115, 252-270.
RfactorNum. reflection% reflection
Rwork0.1557 --
all0.1557 37249 -
obs0.1557 32743 91.5 %
Refinement stepCycle: LAST / Resolution: 1.71→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 124 348 3654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.03
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1
X-RAY DIFFRACTIONp_mcbond_it4.6281
X-RAY DIFFRACTIONp_mcangle_it5.2072
X-RAY DIFFRACTIONp_scbond_it6.1192.5
X-RAY DIFFRACTIONp_scangle_it7.6125
X-RAY DIFFRACTIONp_plane_restr0.0190.03
X-RAY DIFFRACTIONp_chiral_restr0.2470.3
X-RAY DIFFRACTIONp_singtor_nbd0.1640.2
X-RAY DIFFRACTIONp_multtor_nbd0.1450.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2
X-RAY DIFFRACTIONp_xyhbond_nbd0.1450.2
X-RAY DIFFRACTIONp_planar_tor3.76
X-RAY DIFFRACTIONp_staggered_tor14.710
X-RAY DIFFRACTIONp_transverse_tor30.810
X-RAY DIFFRACTIONp_special_tor6
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
1.71-1.850.203X-RAY DIFFRACTION2794
1.85-20.171X-RAY DIFFRACTION5131
2-2.250.159X-RAY DIFFRACTION6930
2.25-2.70.159X-RAY DIFFRACTION7409
2.7-3.40.147X-RAY DIFFRACTION5266
3.4-100.147X-RAY DIFFRACTION5213

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